class12
Stefanie Hodapp (PID: A53300084)
11/5/2021
Working with bio3d
library(bio3d)
pdb <- read.pdb("1hel")## Note: Accessing on-line PDB filepdb##
## Call: read.pdb(file = "1hel")
##
## Total Models#: 1
## Total Atoms#: 1186, XYZs#: 3558 Chains#: 1 (values: A)
##
## Protein Atoms#: 1001 (residues/Calpha atoms#: 129)
## Nucleic acid Atoms#: 0 (residues/phosphate atoms#: 0)
##
## Non-protein/nucleic Atoms#: 185 (residues: 185)
## Non-protein/nucleic resid values: [ HOH (185) ]
##
## Protein sequence:
## KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
## RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
## QAWIRGCRL
##
## + attr: atom, xyz, seqres, helix, sheet,
## calpha, remark, callhead(pdb$atom)## type eleno elety alt resid chain resno insert x y z o b
## 1 ATOM 1 N <NA> LYS A 1 <NA> 3.294 10.164 10.266 1 11.18
## 2 ATOM 2 CA <NA> LYS A 1 <NA> 2.388 10.533 9.168 1 9.68
## 3 ATOM 3 C <NA> LYS A 1 <NA> 2.438 12.049 8.889 1 14.00
## 4 ATOM 4 O <NA> LYS A 1 <NA> 2.406 12.898 9.815 1 14.00
## 5 ATOM 5 CB <NA> LYS A 1 <NA> 0.949 10.101 9.559 1 13.29
## 6 ATOM 6 CG <NA> LYS A 1 <NA> -0.050 10.621 8.573 1 13.52
## segid elesy charge
## 1 <NA> N <NA>
## 2 <NA> C <NA>
## 3 <NA> C <NA>
## 4 <NA> O <NA>
## 5 <NA> C <NA>
## 6 <NA> C <NA>Let’s do a quick bioinformatics prediction of protein dynamics (flexibility). We use the ‘nma()’ function, which does Normal Mode Analysis.
modes <- nma(pdb)## Building Hessian... Done in 0.018 seconds.
## Diagonalizing Hessian... Done in 0.109 seconds.plot(modes)
Make a trajectory of this prediction with the ‘mktrj()’.
mktrj(modes, file="nma.pdb")And the image from VMD
Comparative Structure Analysis
aa <- get.seq("1AKE_A")## Warning in get.seq("1AKE_A"): Removing existing file: seqs.fasta## Fetching... Please wait. Done.aa## 1 . . . . . 60
## pdb|1AKE|A MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT
## 1 . . . . . 60
##
## 61 . . . . . 120
## pdb|1AKE|A DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRI
## 61 . . . . . 120
##
## 121 . . . . . 180
## pdb|1AKE|A VGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIG
## 121 . . . . . 180
##
## 181 . . . 214
## pdb|1AKE|A YYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG
## 181 . . . 214
##
## Call:
## read.fasta(file = outfile)
##
## Class:
## fasta
##
## Alignment dimensions:
## 1 sequence rows; 214 position columns (214 non-gap, 0 gap)
##
## + attr: id, ali, callI want to search the PDB database (the main db for exp structures) for sequences like my aa sequence.
blast <- blast.pdb(aa)## Searching ... please wait (updates every 5 seconds) RID = SB9DGW2M01R
## .
## Reporting 100 hitshits <- plot(blast)## * Possible cutoff values: 197 -3
## Yielding Nhits: 16 100
##
## * Chosen cutoff value of: 197
## Yielding Nhits: 16
Now I have my top hits from the search of the PDB
hits$pdb.id## [1] "1AKE_A" "4X8M_A" "6S36_A" "6RZE_A" "4X8H_A" "3HPR_A" "1E4V_A" "5EJE_A"
## [9] "1E4Y_A" "3X2S_A" "6HAP_A" "6HAM_A" "4K46_A" "4NP6_A" "3GMT_A" "4PZL_A"Here we download all these similar structures in the PDB and store them on our computer
# Download releated PDB files
files <- get.pdb(hits$pdb.id, path="pdbs", split=TRUE, gzip=TRUE)## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 1AKE.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 4X8M.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 6S36.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 6RZE.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 4X8H.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 3HPR.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 1E4V.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 5EJE.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 1E4Y.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 3X2S.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 6HAP.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 6HAM.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 4K46.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 4NP6.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 3GMT.pdb.gz exists. Skipping download## Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE): pdbs/
## 4PZL.pdb.gz exists. Skipping download##
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|======================================================================| 100%We will use the pdbaln() function to align and also optionally fit (i.e. superpose) the identified PDB structures
# Align related PDBs
pdbs <- pdbaln(files, fit = TRUE)## Reading PDB files:
## pdbs/split_chain/1AKE_A.pdb
## pdbs/split_chain/4X8M_A.pdb
## pdbs/split_chain/6S36_A.pdb
## pdbs/split_chain/6RZE_A.pdb
## pdbs/split_chain/4X8H_A.pdb
## pdbs/split_chain/3HPR_A.pdb
## pdbs/split_chain/1E4V_A.pdb
## pdbs/split_chain/5EJE_A.pdb
## pdbs/split_chain/1E4Y_A.pdb
## pdbs/split_chain/3X2S_A.pdb
## pdbs/split_chain/6HAP_A.pdb
## pdbs/split_chain/6HAM_A.pdb
## pdbs/split_chain/4K46_A.pdb
## pdbs/split_chain/4NP6_A.pdb
## pdbs/split_chain/3GMT_A.pdb
## pdbs/split_chain/4PZL_A.pdb
## PDB has ALT records, taking A only, rm.alt=TRUE
## .. PDB has ALT records, taking A only, rm.alt=TRUE
## . PDB has ALT records, taking A only, rm.alt=TRUE
## .. PDB has ALT records, taking A only, rm.alt=TRUE
## .. PDB has ALT records, taking A only, rm.alt=TRUE
## .... PDB has ALT records, taking A only, rm.alt=TRUE
## . PDB has ALT records, taking A only, rm.alt=TRUE
## ....
##
## Extracting sequences
##
## pdb/seq: 1 name: pdbs/split_chain/1AKE_A.pdb
## PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 2 name: pdbs/split_chain/4X8M_A.pdb
## pdb/seq: 3 name: pdbs/split_chain/6S36_A.pdb
## PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 4 name: pdbs/split_chain/6RZE_A.pdb
## PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 5 name: pdbs/split_chain/4X8H_A.pdb
## pdb/seq: 6 name: pdbs/split_chain/3HPR_A.pdb
## PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 7 name: pdbs/split_chain/1E4V_A.pdb
## pdb/seq: 8 name: pdbs/split_chain/5EJE_A.pdb
## PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 9 name: pdbs/split_chain/1E4Y_A.pdb
## pdb/seq: 10 name: pdbs/split_chain/3X2S_A.pdb
## pdb/seq: 11 name: pdbs/split_chain/6HAP_A.pdb
## pdb/seq: 12 name: pdbs/split_chain/6HAM_A.pdb
## PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 13 name: pdbs/split_chain/4K46_A.pdb
## PDB has ALT records, taking A only, rm.alt=TRUE
## pdb/seq: 14 name: pdbs/split_chain/4NP6_A.pdb
## pdb/seq: 15 name: pdbs/split_chain/3GMT_A.pdb
## pdb/seq: 16 name: pdbs/split_chain/4PZL_A.pdbLet’s look at our alignment
pdbs## 1 . . . 40
## [Truncated_Name:1]1AKE_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:2]4X8M_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:3]6S36_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:4]6RZE_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:5]4X8H_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:6]3HPR_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:7]1E4V_A.pdb ----------MRIILLGAPVAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:8]5EJE_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:9]1E4Y_A.pdb ----------MRIILLGALVAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:10]3X2S_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:11]6HAP_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:12]6HAM_A.pdb ----------MRIILLGAPGAGKGTQAQFIMEKYGIPQIS
## [Truncated_Name:13]4K46_A.pdb ----------MRIILLGAPGAGKGTQAQFIMAKFGIPQIS
## [Truncated_Name:14]4NP6_A.pdb --------NAMRIILLGAPGAGKGTQAQFIMEKFGIPQIS
## [Truncated_Name:15]3GMT_A.pdb ----------MRLILLGAPGAGKGTQANFIKEKFGIPQIS
## [Truncated_Name:16]4PZL_A.pdb TENLYFQSNAMRIILLGAPGAGKGTQAKIIEQKYNIAHIS
## **^***** ******* * *^ * **
## 1 . . . 40
##
## 41 . . . 80
## [Truncated_Name:1]1AKE_A.pdb TGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKE
## [Truncated_Name:2]4X8M_A.pdb TGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKE
## [Truncated_Name:3]6S36_A.pdb TGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKE
## [Truncated_Name:4]6RZE_A.pdb TGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKE
## [Truncated_Name:5]4X8H_A.pdb TGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKE
## [Truncated_Name:6]3HPR_A.pdb TGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKE
## [Truncated_Name:7]1E4V_A.pdb TGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKE
## [Truncated_Name:8]5EJE_A.pdb TGDMLRAAVKSGSELGKQAKDIMDACKLVTDELVIALVKE
## [Truncated_Name:9]1E4Y_A.pdb TGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKE
## [Truncated_Name:10]3X2S_A.pdb TGDMLRAAVKSGSELGKQAKDIMDCGKLVTDELVIALVKE
## [Truncated_Name:11]6HAP_A.pdb TGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVRE
## [Truncated_Name:12]6HAM_A.pdb TGDMLRAAIKSGSELGKQAKDIMDAGKLVTDEIIIALVKE
## [Truncated_Name:13]4K46_A.pdb TGDMLRAAIKAGTELGKQAKSVIDAGQLVSDDIILGLVKE
## [Truncated_Name:14]4NP6_A.pdb TGDMLRAAIKAGTELGKQAKAVIDAGQLVSDDIILGLIKE
## [Truncated_Name:15]3GMT_A.pdb TGDMLRAAVKAGTPLGVEAKTYMDEGKLVPDSLIIGLVKE
## [Truncated_Name:16]4PZL_A.pdb TGDMIRETIKSGSALGQELKKVLDAGELVSDEFIIKIVKD
## ****^* ^* *^ ** * ^* ** * ^^ ^^^^
## 41 . . . 80
##
## 81 . . . 120
## [Truncated_Name:1]1AKE_A.pdb RIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:2]4X8M_A.pdb RIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:3]6S36_A.pdb RIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:4]6RZE_A.pdb RIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:5]4X8H_A.pdb RIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:6]3HPR_A.pdb RIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:7]1E4V_A.pdb RIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:8]5EJE_A.pdb RIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:9]1E4Y_A.pdb RIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:10]3X2S_A.pdb RIAQEDSRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:11]6HAP_A.pdb RICQEDSRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:12]6HAM_A.pdb RICQEDSRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFD
## [Truncated_Name:13]4K46_A.pdb RIAQDDCAKGFLLDGFPRTIPQADGLKEVGVVVDYVIEFD
## [Truncated_Name:14]4NP6_A.pdb RIAQADCEKGFLLDGFPRTIPQADGLKEMGINVDYVIEFD
## [Truncated_Name:15]3GMT_A.pdb RLKEADCANGYLFDGFPRTIAQADAMKEAGVAIDYVLEID
## [Truncated_Name:16]4PZL_A.pdb RISKNDCNNGFLLDGVPRTIPQAQELDKLGVNIDYIVEVD
## *^ * *^* ** **** ** ^ *^ ^**^^* *
## 81 . . . 120
##
## 121 . . . 160
## [Truncated_Name:1]1AKE_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:2]4X8M_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:3]6S36_A.pdb VPDELIVDKIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:4]6RZE_A.pdb VPDELIVDAIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:5]4X8H_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:6]3HPR_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDGTG
## [Truncated_Name:7]1E4V_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:8]5EJE_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:9]1E4Y_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:10]3X2S_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:11]6HAP_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:12]6HAM_A.pdb VPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTG
## [Truncated_Name:13]4K46_A.pdb VADSVIVERMAGRRAHLASGRTYHNVYNPPKVEGKDDVTG
## [Truncated_Name:14]4NP6_A.pdb VADDVIVERMAGRRAHLPSGRTYHVVYNPPKVEGKDDVTG
## [Truncated_Name:15]3GMT_A.pdb VPFSEIIERMSGRRTHPASGRTYHVKFNPPKVEGKDDVTG
## [Truncated_Name:16]4PZL_A.pdb VADNLLIERITGRRIHPASGRTYHTKFNPPKVADKDDVTG
## * ^^^ ^ *** * *** ** ^***** *** **
## 121 . . . 160
##
## 161 . . . 200
## [Truncated_Name:1]1AKE_A.pdb EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:2]4X8M_A.pdb EELTTRKDDQEETVRKRLVEWHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:3]6S36_A.pdb EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:4]6RZE_A.pdb EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:5]4X8H_A.pdb EELTTRKDDQEETVRKRLVEYHQMTAALIGYYSKEAEAGN
## [Truncated_Name:6]3HPR_A.pdb EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:7]1E4V_A.pdb EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:8]5EJE_A.pdb EELTTRKDDQEECVRKRLVEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:9]1E4Y_A.pdb EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:10]3X2S_A.pdb EELTTRKDDQEETVRKRLCEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:11]6HAP_A.pdb EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:12]6HAM_A.pdb EELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGN
## [Truncated_Name:13]4K46_A.pdb EDLVIREDDKEETVLARLGVYHNQTAPLIAYYGKEAEAGN
## [Truncated_Name:14]4NP6_A.pdb EDLVIREDDKEETVRARLNVYHTQTAPLIEYYGKEAAAGK
## [Truncated_Name:15]3GMT_A.pdb EPLVQRDDDKEETVKKRLDVYEAQTKPLITYYGDWARRGA
## [Truncated_Name:16]4PZL_A.pdb EPLITRTDDNEDTVKQRLSVYHAQTAKLIDFYRNFSSTNT
## * * * ** *^ * ** ^ * ** ^*
## 161 . . . 200
##
## 201 . . 227
## [Truncated_Name:1]1AKE_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:2]4X8M_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:3]6S36_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:4]6RZE_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:5]4X8H_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:6]3HPR_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:7]1E4V_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:8]5EJE_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:9]1E4Y_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:10]3X2S_A.pdb T--KYAKVDGTKPVAEVRADLEKILG-
## [Truncated_Name:11]6HAP_A.pdb T--KYAKVDGTKPVCEVRADLEKILG-
## [Truncated_Name:12]6HAM_A.pdb T--KYAKVDGTKPVCEVRADLEKILG-
## [Truncated_Name:13]4K46_A.pdb T--QYLKFDGTKAVAEVSAELEKALA-
## [Truncated_Name:14]4NP6_A.pdb T--QYLKFDGTKQVSEVSADIAKALA-
## [Truncated_Name:15]3GMT_A.pdb E-------NGLKAPA-----YRKISG-
## [Truncated_Name:16]4PZL_A.pdb KIPKYIKINGDQAVEKVSQDIFDQLNK
## *
## 201 . . 227
##
## Call:
## pdbaln(files = files, fit = TRUE)
##
## Class:
## pdbs, fasta
##
## Alignment dimensions:
## 16 sequence rows; 227 position columns (204 non-gap, 23 gap)
##
## + attr: xyz, resno, b, chain, id, ali, resid, sse, call# Vector containing PDB codes for figure axis
ids <- basename.pdb(pdbs$id)
# Draw schematic alignment
plot(pdbs, labels=ids)
pdbs$xyz##
## Total Frames#: 16
## Total XYZs#: 681, (Atoms#: 227)
##
## [1] NA NA NA <...> 15.818 46.771 47.7 [10896]
##
## + attr: Matrix DIM = 16 x 681Principal Component Analysis (PCA)
Here we will do PCA on the xyz coordinate data of all these structures with the ‘pca()’ function in bio3d
pc <- pca(pdbs)
plot(pc)
Let’s visualize the displacements (i.e. movements of the structure) that are captured by PC1
mktrj(pc, pc=1, file="pca.pdb")
Let’s save our important results
# save(blast, hits, pca, file="myresults.RData")
load("myresults.RData")